[MAINT] pre-release 0.2.0 #647
Commits on Jul 9, 2022
Commits on Jul 10, 2022
Commits on Jul 11, 2022
-
Merge branch 'master' of https://github.com/bids-standard/bids-matlab …
…into transformers
-
Commits on Jul 20, 2022
-
Merge pull request #405 from Remi-Gau/transformers
[ENH] upgrade transformers
Commits on Jul 29, 2022
Commits on Jul 30, 2022
-
-
Merge pull request #410 from Remi-Gau/dev
[FIX] fix bugs in setting modality and getting entity order from schema
Commits on Aug 24, 2022
Commits on Aug 29, 2022
Commits on Sep 8, 2022
-
-
-
Merge pull request #422 from bids-standard/layout
[ENH] make layout more verbose and warning more informative
Commits on Sep 9, 2022
-
-
-
-
Merge pull request #426 from Remi-Gau/participants
[ENH] add simple function to create participants.tsv
Commits on Sep 11, 2022
Commits on Oct 17, 2022
Commits on Oct 21, 2022
-
-
Merge pull request #444 from Remi-Gau/infra
[MNT] clean up maintenance and contributing doc
-
Merge pull request #378 from bids-standard/demo_File
[DOC] add demo script for bids.File
-
-
-
Commits on Oct 22, 2022
-
-
-
-
-
-
-
-
Merge pull request #447 from Remi-Gau/doc
[DOC] add script version of the notebooks and update help sections
Commits on Nov 4, 2022
-
-
[pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
-
-
-
Commits on Nov 7, 2022
Commits on Nov 8, 2022
-
-
-
-
-
[pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
-
-
Merge pull request #466 from Remi-Gau/win_fix
[FIX] windows related fixes
-
-
Merge pull request #463 from Remi-Gau/update_dataset
[ENH] add create sessions and create scans functionalities
-
-
-
-
Commits on Nov 9, 2022
-
Merge pull request #472 from bids-standard/error_msg
[MISC] improve error message
Commits on Nov 11, 2022
Commits on Nov 13, 2022
-
-
-
-
Merge pull request #481 from bids-standard/list_trial_types
[FIX] List trial types
-
-
Merge pull request #484 from bids-standard/download
[FIX] make download more robust when wget is not present
-
-
Merge pull request #483 from bids-standard/derivatives
[FIX] handle create derivatives metadata when some entity labels are just a number
Commits on Nov 14, 2022
-
-
-
Merge pull request #486 from bids-standard/win_path
[FIX] reformat windows path when printing to avoiding escaped characters wa…
Commits on Nov 16, 2022
-
-
Merge pull request #487 from bids-standard/init_ses
[FIX] fix create sessions and participants tsv
Commits on Nov 17, 2022
Commits on Nov 18, 2022
Commits on Nov 19, 2022
-
Merge pull request #488 from Remi-Gau/dev
[ENH] add datalad related hints when file writing fails
Commits on Nov 25, 2022
Commits on Dec 10, 2022
-
Merge pull request #497 from bids-standard/master
[MNT] merge master in dev
Commits on Dec 13, 2022
-
-
Merge pull request #498 from bids-standard/trans
[ENH] improve transformers
Commits on Dec 26, 2022
Commits on Dec 27, 2022
-
-
-
-
-
-
-
-
-
-
-
Merge pull request #503 from Remi-Gau/init
[ENH] validate folder name in bids.init
-
Merge pull request #502 from Remi-Gau/datalad
[ENH] better handling of datalad datasets
-
-
-
Merge pull request #501 from bids-standard/events
[ENH] improve events plotting
Commits on Dec 29, 2022
-
-
-
-
Merge pull request #504 from Remi-Gau/events_diag
[ENH] add diagnostic for events
Commits on Jan 5, 2023
Commits on Jan 6, 2023
-
-
Merge pull request #506 from Remi-Gau/transformer_rules
[REF] refactor transformer rules
-
Merge pull request #507 from bids-standard/facerep
[FIX] use trial_type for the facerep conversion script
Commits on Jan 18, 2023
-
-
-
-
Merge pull request #509 from bids-standard/silence
[ENH] add flags to make some functions less verbose
Commits on Jan 22, 2023
-
-
-
-
-
Merge pull request #510 from bids-standard/filter_layout
[ENH] Filter layout
Commits on Feb 7, 2023
-
Merge pull request #517 from bids-standard/master
[INFRA] update schema in dev
Commits on Feb 15, 2023
-
-
-
-
-
-
-
-
-
-
-
Merge pull request #518 from bids-standard/test_octave
[INFRA] improve octave support for transformers
-
-
Commits on Feb 16, 2023
-
Merge pull request #519 from bids-standard/download
[INFRA] make download use urlwrite first and fall back on wget
Commits on Mar 28, 2023
-
-
-
Merge pull request #530 from Remi-Gau/update_dev
[MAINT] add pre commit hooks
-
Merge pull request #531 from Remi-Gau/fix-schema_dev
[FIX] update schema related tests
Commits on Mar 29, 2023
-
Merge pull request #532 from bids-standard/fix-filter_transformer
[FIX] transformers with "filter" should not fail when filtering variable is missing
Commits on Apr 20, 2023
-
[DOC] update bids.layout doc and return_file_index error message (#539)
* update doc * add more detail when error happens in return_file_index * update precommit * update pre-commit and run on all files
Commits on Apr 21, 2023
-
[ENH] update warning message on return_file_index failure (#540)
* update doc * add more detail when error happens in return_file_index * update precommit * update pre-commit and run on all files * update warning * improve error message
Commits on Apr 27, 2023
-
-
[MAINT] back merge master (#549)
* docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * CI: Use PAT to submit pull requests (#534) This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions. * Bump peter-evans/create-pull-request from 4 to 5 (#536) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#548) * update schema * readd token$ --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
4 people authoredApr 27, 2023 -
[FIX] failing to return file index during dependencies indexing thorw…
… warning and not error (#546) * no file index throws warning and not error * silence octave warning
Commits on Apr 28, 2023
-
-
[ENH] support querying for scans.tsv and sessions.tsv (#550)
* add querying for scans * add querying for sessions * count sessions and scans as suffixes * fix tests
-
[ENH] allow to query directly for tsv content (#555)
* silence some warnings * test error
Commits on May 1, 2023
Commits on May 5, 2023
-
[INFRA] run tests on mac OS and windows for matlab (#560)
* docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * CI: Use PAT to submit pull requests (#534) This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions. * Bump peter-evans/create-pull-request from 4 to 5 (#536) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#548) * update schema * readd token$ * update ci (#558) * split workflows matlab and octave * fix * use shorthand for commands * skip coverage on windows * [FIX] remove byte order mark from tsv file (#556) * fix bom * add data * octave fix * change the way CI is detected * fix tests * sanitize path in error * [DATALAD] Recorded changes * [DATALAD] Recorded changes --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
4 people authoredMay 5, 2023
Commits on May 11, 2023
-
[INFRA] randomize tests order (#566)
* randomize tests * fix doc generation and links * skip dead links * skip dead links * skip dead links * skip dead links * use temp_dir
Commits on Jun 12, 2023
-
[MAINT] update schema dev (#580)
* docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * CI: Use PAT to submit pull requests (#534) This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions. * Bump peter-evans/create-pull-request from 4 to 5 (#536) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#548) * update schema * readd token$ * update ci (#558) * [FIX] remove byte order mark from tsv file (#556) * fix bom * add data * octave fix * Bump matlab-actions/run-command from 1.1.3 to 1.2.0 (#570) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.1.3 to 1.2.0. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.1.3...v1.2.0) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#577) * update schema * rm token --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
4 people authoredJun 12, 2023
Commits on Jun 18, 2023
-
[ENH] give more meaningful error messsages when failing to read json (#…
…582) * add warning mentioning which json files could not be read * add file not found erro
-
-
[DOC] update help of several functions (#583)
* update doc * update example * fixes
-
[ENH] add electrodes and optodes as group dependencies (#586)
* add electrodes and optodes as dependencies * inline function * fix
Commits on Jul 31, 2023
-
-
[ENH] index and query phenotype (#590)
* index and query phenotype * do not load content and metadata
-
[ENH] do not add subject to layout if it is empty (#600)
* do not add subject to layout if it is empty * subject is in structure if schemaless * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactor * get properties and not fields when dealing with bids.File instance * rerun * silence failing tests on windows --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
-
[MAINT] Update from main (#606)
* docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * CI: Use PAT to submit pull requests (#534) This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions. * Bump peter-evans/create-pull-request from 4 to 5 (#536) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#548) * update schema * readd token$ * update ci (#558) * [FIX] remove byte order mark from tsv file (#556) * fix bom * add data * octave fix * Bump matlab-actions/run-command from 1.1.3 to 1.2.0 (#570) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.1.3 to 1.2.0. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.1.3...v1.2.0) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#577) * update schema * rm token * docs: add coxroy as a contributor for bug, ideas, and userTesting (#585) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * BIDS schema update (#587) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#592) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#594) Co-authored-by: Remi-Gau <[email protected]> * Bump matlab-actions/run-command from 1.2.0 to 1.2.1 (#602) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.0 to 1.2.1. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.2.0...v1.2.1) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [FIX] handle nan and and datetimes when printing tables (#605) * fix bugs in tables and datetimes * skip on windows * update schema --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <[email protected]>
6 people authoredJul 31, 2023
Commits on Aug 5, 2023
-
[ENH] use inheritance in get_meta_list (#609)
* use inheritance in get_meta_list * refactor
-
[ENH] improve bids schema api (#610)
* improve API * add doc * skip octave for test
-
[FIX] better handle printing of paths in windows (#611)
* better handle printting of paths in windows * fix more paths * more clean up * fix more paths
Commits on Aug 7, 2023
Commits on Aug 8, 2023
-
-
Incorporating json into bids.File (issues #596 #371) (#597)
* First attempt to incorporate json into bids.File * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * lint * Added util function to update structures * Style and tests for util/update_struct.m * Using metadata field instead of json_struct * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed JSONFile subclass * Added tests for metadata for File class * Fixed spelling in doc * File: Added functions that act on individual fields * File: fixed style * Splitted File.metadada tests into smaller ones --------- Co-authored-by: Beliy Nikita <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Gau <[email protected]>
4 people authoredAug 8, 2023
Commits on Aug 12, 2023
Commits on Aug 13, 2023
Commits on Aug 18, 2023
-
[ENH] improve performance and testing (#618)
* update timing * try speed up test by not indexing dependencies * run on latest and oldest matlab * [DATALAD] Recorded changes * [DATALAD] Recorded changes * cancel previous runs * speed up some tests or functions * run slow and fast tests in parallel * windows env var fix * try using globals * fix * add more slow test * add doc
Commits on Aug 22, 2023
Commits on Aug 26, 2023
-
[ENH] remove atlas and update res and den metadata (#622)
* rm atlas and update res and den metadata * fix
Commits on Sep 4, 2023
Commits on Sep 6, 2023
-
[FIX] Fix tests after merge from master (#627)
* fix tests after merge from main * fix test octave
Commits on Sep 16, 2023
Commits on Nov 6, 2023
-
[MAINT] merge main in dev (#644)
* BIDS schema update (#628) Co-authored-by: Remi-Gau <[email protected]> * Bump actions/checkout from 3 to 4 (#629) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * BIDS schema update (#633) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#634) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#635) Co-authored-by: Remi-Gau <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#636) updates: - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BIDS schema update (#637) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#639) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#640) Co-authored-by: Remi-Gau <[email protected]> * Bump matlab-actions/setup-matlab from 1.2.4 to 1.2.5 (#641) Bumps [matlab-actions/setup-matlab](https://github.com/matlab-actions/setup-matlab) from 1.2.4 to 1.2.5. - [Release notes](https://github.com/matlab-actions/setup-matlab/releases) - [Commits](matlab-actions/setup-matlab@v1.2.4...v1.2.5) --- updated-dependencies: - dependency-name: matlab-actions/setup-matlab dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump matlab-actions/run-command from 1.2.1 to 1.2.2 (#642) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.1 to 1.2.2. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.2.1...v1.2.2) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [FIX] update test after schema update (#643) * fix test after schema update * set os version for doc * update schema * fix typos * update tests --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
5 people authoredNov 6, 2023